On 23 September 2018, Flanagan played for Newtown in the Intrust Super Premiership NSW grand final defeat against Canterbury.

[2] In Round 13 of the 2019 NRL season, Flanagan scored 18 individual points which included a try and seven goals as Cronulla defeated Parramatta 42-22 at Shark Park.

Flanagan played a total of 20 games for the Sydney Roosters in the 2020 NRL season as the club finished fourth on the table.

[8] In round 9 of the 2021 NRL season, Flanagan was substituted off the field by Canterbury head coach Trent Barrett after a poor first half performance in the club's 32-12 loss against St.

[9] Flanagan was then dropped from the first grade team until the round 16 game against Manly Warringah Sea Eagles, when he was reselected after four Canterbury players were side-lined by NSW Health after breaching NRL restrictions related to COVID-19.